Extensions starts with a dot

[marberi]

When attempting to motioncorrect data in a zarr file, then:
MotionCorrect(fname)

claim the extension was not found. It should be ".zarr" and ".n5" with
dots at the beginning. Including this fix uncovers a different problem
later (zarr array does not have .keys()).

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would break back-compatibility)
• Changes in documentation or new examples for demos and/or use cases.

Branching

• All PRs should be made against the dev branch. The main branch is not often merged back to dev.
• If you want to get your PR out to the world faster (urgent bugfix), poke pgunn to cut a release; this will get it onto github and into conda faster

Has your PR been tested?

If you're fixing a bug or introducing a new feature it is recommended you run the tests by typing

caimanmanager test

and

caimanmanager demotest

prior to submitting your pull request.

Please describe any additional tests that you ran to verify your changes. If they are fast you can also
include them in the folder 'caiman/tests/and name themtest_***.py` so they can be included in our lists of tests.

[pgunn]

I am likely to merge this today.

Regarding the further-downstream issues you found, I think locally I converted some of our test data to n5 and zarr and run the pipeline on them, but my process may not have been through enough; do you have handy the exact error messages you got? (if you have sample data and params that go with them that'd also be great).

[marberi]

I don't have it readily available. For getting some results I did some workaround...

[EmeEmu]

Hey, this is still not available in the main branch. Are you planning on merging ?
In the meantime, @marberi what was your workaround ?
thanks !

[pgunn]

Give me a moment to figure out what happened here; it was merged into dev and is in the history, but the changes are not present for some reason. I wonder if I messed up some merge conflict.

[pgunn]

@EmeEmu @marberi
I think I messed up resolving a merge conflict that resulted in this diff being un-applied due to other work I was doing on the same code. I will add it back in, and try to get a new release out soon. Sorry for the fuss.

[pgunn]

Actually, no. The issue is that this change needed to be made in two separate parts of the file (that look very similar to each other), and this diff only covered one of them. I'll fix the other (around line 1520). Thanks for bringing it to my attention.

[EmeEmu]

thanks @pgunn !

As mentioned previously @marberi, solving this leads to another error down the line :
AttributionError: 'Array' object has no attribute 'keys'
I haven't yet looked into possible solutions for this. If you want I can open a new issue.

[pgunn]

Please do, and include the full text of the error and the backtrace. That'll help me track down where it is.